Insertion of 5-methyl-N-(1-pyrenylmethyl)cytidine into DNA. Duplex, three-way junction and triplex stabilities

5′-O-(4,4′-dimethoxytrityl)-5-methyl-N⁴-(1-pyrenylmethyl)cytidine(5) was prepared by reaction of 1-pyrenylmethylamine with an appropriate protected 4-(1,2,4-triazolyl)thymidine derivative which was synthesized from 5-O-DMT protected thymidine by acetylation with acetic anhydride and subsequent reaction with triethylamine, 1,2,4-triazole and POCl₃. Stabilities are reported for DNA duplexes, three-way junctions and triplexes when 5 is inserted. Most interestingly, the three-way junctions are stabilized when 5 is used for insertion into the junction region. This break-through for recognizing the foot of a stem could have far-reaching importance because new targets for antisense oligos is now rendered possible on intact secondary structures.